The U.S. Federal Energy Regulatory Commission has yet to mandate incorporation of anticipated climate change effects on hydropower system operations when assessing environmental impacts from the renewal of hydropower licenses. One stated reason is the lack of specific project-level specificity in future impacts. We demonstrate how a hydropower system operations model, incorporating the latest climatological realizations (3 GCMs x RCPs 4.5 and 8.5), can be used to assess environmental impacts generally, and hydrological flow alterations in particular, during the hydropower licensing process. We demonstrate that we can, in fact, quantify project-level impacts from climate change, albeit within the context of quantified uncertainty about non-stationary future conditions. The systems operations model analysis encompasses the combined effects of the Yuba River Development Project and Yuba-Bear Drum-Spaulding Projects, an interconnected series of complex hydropower systems located in the Sierra Nevada, California. Daily water system operations are simulated using a monthly-scale optimization model for hydropower decisions. Though there is inherent uncertainty generated by the modeling process and operational assumptions (e.g., static energy demand), there are sufficient data, modeling techniques, and analytical approaches to assess the how management decisions made today may be confounded by non-stationary hydroclimates in 30-50 years, which is the duration of most hydropower licenses. Such decisions need to include adaptive management approaches to address not only non-stationary hydroclimates, but also cumulative impacts to ecological functions and processes caused by serial flow manipulation. This study can help provide the scientific guidance needed to improve climate change policy in hydropower system planning.